SiR-Tubulin Kit

SiR-Tubulin Kit

SiR-tubulin is based on the microtubule binding drug Docetaxel. SiR-tubulin is fluorogenic, cell permeable and highly specific for microtubules. Sir-tubulin stains endogenous microtubules without the need for genetic manipulation or overexpression. Its emission in the far red minimizes phototoxicity and sample autofluorescence. SiR-tubulin is compatible with GFP and/or m-cherry fluorescent proteins. It can be imaged with standard Cy5 filtersets. SiR-tubulin can be used for widefield, confocal, SIM or STED imaging in living cells and tissue. Probe quantity allows 50 – 300 staining experiments.*



Optical properties

λabs   652 nm

λEm   674 nm
εmax 1.0·105 mol-1·cm-1

*Based on the following conditions: 0.3 – 1 ml staining solution / staining experiments with 0.5 – 1 uM probe concentration. The number of staining experiments can be further increased by reducing volume or probe concentration.

Cytoskeleton, Inc. is the exclusive provider of Spirochrome, Ltd. products in North America.

For product Datasheets and MSDSs please click on the PDF links below.

Spirochrome Technical Tips and Ex/Em spectra in graphical form (PDF)

AuthorTitleJournalYearArticle Link
Joseph, Ivor et al.RAB11A and RAB11B control mitotic spindle function in intestinal epithelial progenitor cellsEMBO reports2023ISSN 1469--221X
Sanchini, Caterina et al.Protocol for observing microtubules and microtubule ends in both fixed and live primary microglia cellsSTAR Protocols2023ISSN 2666--1667
Richter, Manuela et al.Kinetochore-fiber lengths are maintained locally but coordinated globally by poles in the mammalian spindleeLife2023ISSN 2050-084X
Dang, David et al.Deep learning techniques and mathematical modeling allow 3D analysis of mitotic spindle dynamicsThe Journal of cell biology2023ISSN 1540-8140
Dunkley, Sam et al.Actin limits egg aneuploidies associated with female reproductive agingScience Advances2023ISSN 2375-2548
Alvelid, Jonatan et al.Event-triggered STED imagingNature Methods 2022 19:102022ISSN 1548--7105
Králová, J et al.Sterolight as imaging tool to study sterol uptake, trafficking and efflux in living cellsScientific Reports2022Article Link
Dema, Alessandro et al.Optogenetic EB1 inactivation shortens metaphase spindles by disrupting cortical force-producing interactions with astral microtubulesCurrent Biology2022ISSN 1879-0445
Kemble, Samuel et al.Analysis of Preplatelets and Their Barbell Platelet Derivatives by Imaging Flow CytometryBlood Advances2022ISSN 2473--9529
Safieddine, Adham et al.A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transportNature Communications 2021 12:12021ISSN 2041--1723
Scherer, Katharina M. et al.A fluorescent reporter system enables spatiotemporal analysis of host cell modification during herpes simplex virus-1 replication2021PMID 33380421
Tsuchiya, Kenta et al.Ran-GTP Is Non-essential to Activate NuMA for Mitotic Spindle-Pole Focusing but Dynamically Polarizes HURP Near ChromosomesCurrent Biology2021ISSN 1879-0445
Kalargyrou, Aikaterini A et al.Nanotube‐like processes facilitate material transfer between photoreceptorsEMBO reports2021ISSN 1469--221X
Watson, Joseph L. et al.High-efficacy subcellular micropatterning of proteins using fibrinogen anchorsJournal of Cell Biology2021ISSN 1540-8140
Ho, Chi Nguyen Quynh et al.Simulated Microgravity Inhibits the Proliferation of Chang Liver Cells by Attenuation of the Major Cell Cycle Regulators and Cytoskeletal ProteinsInternational Journal of Molecular Sciences 2021, Vol. 22, Page 45502021ISSN 1422--0067
Gurianov, D. S. et al.PH domain of BCR provides colocalization of full-length BCR with centrosome together with cortactin to facilitate actin-organizing functionBiopolymers and Cell2021ISSN 0233--7657
Fiege, Jessica K. et al.Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epitheliumPLOS Pathogens2021ISSN 1553--7374
Wolf, Bas de et al.Chromosomal instability by mutations in the novel minor spliceosome component CENATACThe EMBO Journal2021ISSN 1460--2075
Siddiqui, Sana et al.Epithelial miR-141 regulates IL-13–induced airway mucus productionJCI Insight2021ISSN 0021--9738
Blengini, Cecilia S. et al.Aurora kinase A is essential for meiosis in mouse oocytesPLOS Genetics2021ISSN 1553--7404
Hao, Kai et al.Cilia locally synthesize proteins to sustain their ultrastructure and functionsNature Communications2021ISSN 2041-1723
Miao, Shumin et al.DIAPH1 regulates chromosomal instability of cancer cells by controlling microtubule dynamicsEuropean Journal of Cell Biology2021ISSN 1618-1298
Singh, Divya et al.Destabilization of Long Astral Microtubules via Cdk1-Dependent Removal of GTSE1 from Their Plus Ends Facilitates Prometaphase Spindle OrientationCurrent Biology2021ISSN 1879-0445
Buijs, Robin R. et al.WDR47 protects neuronal microtubule minus ends from katanin-mediated severingCell Reports2021ISSN 2211-1247
Hoffmann, Patrick C. et al.Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoidseLife2021ISSN 2050-084X
Jagrić, Mihaela et al.Optogenetic control of prc1 reveals its role in chromosome alignment on the spindle by overlap length-dependent forceseLife2021ISSN 2050-084X
Chinen, Takumi et al.Centriole and PCM cooperatively recruit CEP192 to spindle poles to promote bipolar spindle assemblyJournal of Cell Biology2021ISSN 1540-8140
Quidwai, Tooba et al.A WDR35-dependent coat protein complex transports ciliary membrane cargo vesicles to ciliaeLife2021ISSN 2050-084X
Klemm, Lucas C. et al.Centriole and Golgi microtubule nucleation are dispensable for the migration of human neutrophil-like cellsMolecular Biology of the Cell2021ISSN 1939-4586
Zhao, Huijie et al.Fibrogranular materials function as organizers to ensure the fidelity of multiciliary assemblyNature Communications2021ISSN 2041-1723
Ordureau, Alban et al.Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagyMolecular Cell2021ISSN 1097-4164
Schiweck, Juliane et al.Drebrin controls scar formation and astrocyte reactivity upon traumatic brain injury by regulating membrane traffickingNature Communications2021ISSN 2041-1723
Vukušić, Kruno et al.Microtubule-sliding modules based on kinesins EG5 and PRC1-dependent KIF4A drive human spindle elongationDevelopmental Cell2021ISSN 1878-1551
Lv, Qi et al.RNA-binding protein SORBS2 suppresses clear cell renal cell carcinoma metastasis by enhancing MTUS1 mRNA stabilityCell Death & Disease 2020 11:122020ISSN 2041--4889
Tabdanov, Erdem D. et al.Engineering Elastic Nano- and Micro-Patterns and Textures for Directed Cell MotilitySTAR Protocols2020ISSN 2666--1667
Ueki, Hiroshi et al.Multicolor two-photon imaging of in vivo cellular pathophysiology upon influenza virus infection using the two-photon IMPRESSNature Protocols2020ISSN 1754--2189
Park, Yeonkyoung et al.Nonsense-mediated mRNA decay factor UPF1 promotes aggresome formationNature Communications2020ISSN 2041-1723
Drutovic, David et al. Ran GTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes The EMBO Journal2020ISSN 0261--4189
Cao, Yujie et al.Microtubule Minus-End Binding Protein CAMSAP2 and Kinesin-14 Motor KIFC3 Control Dendritic Microtubule OrganizationCurrent Biology2020ISSN 1879-0445
Afanzar, Oshri et al.The nucleus serves as the pacemaker for the cell cycleeLife2020ISSN 2050-084X
Chinen, Takumi et al. Nu MA assemblies organize microtubule asters to establish spindle bipolarity in acentrosomal human cells The EMBO Journal2020ISSN 0261--4189
Hégarat, Nadia et al.Cyclin A triggers Mitosis either via the Greatwall kinase pathway or Cyclin BThe EMBO Journal2020ISSN 0261--4189
Tona, Yosuke et al.Live imaging of hair bundle polarity acquisition demonstrates a critical timeline for transcription factor EMX2eLife2020ISSN 2050-084X
Domart, Florelle et al.Correlating sted and synchrotron xrf nano-imaging unveils cosegregation of metals and cytoskeleton proteins in dendriteseLife2020ISSN 2050-084X
Stiff, Tom et al.Prophase-Specific Perinuclear Actin Coordinates Centrosome Separation and Positioning to Ensure Accurate Chromosome SegregationCell Reports2020ISSN 2211-1247
Frontalini, F. et al.Foraminiferal Ultrastructure: A perspective From Fluorescent and Fluorogenic ProbesJournal of Geophysical Research: Biogeosciences2019ISSN 2169-8961
Dudka, Damian et al.Spindle-Length-Dependent HURP Localization Allows Centrosomes to Control Kinetochore-Fiber Plus-End DynamicsCurrent Biology2019ISSN 0960-9822
Wagner, Fabienne et al.Armadillo repeat-containing protein 1 is a dual localization protein associated with mitochondrial intermembrane space bridging complexPLoS ONE2019ISSN 1932-6203
Hu, Junyan et al.Distinct roles of two myosins in C. Elegans spermatid differentiationPLoS Biology2019ISSN 1545-7885
Drpic, Danica et al.Chromosome Segregation Is Biased by Kinetochore SizeCurrent Biology2018ISSN 0960-9822
Nguyen, Alexandra L. et al.Genetic Interactions between the Aurora Kinases Reveal New Requirements for AURKB and AURKC during Oocyte MeiosisCurrent Biology2018ISSN 0960-9822
Khatri, Natasha et al.The autism protein Ube3A/E6AP remodels neuronal dendritic arborization via caspase-dependent microtubule destabilizationJournal of Neuroscience2018ISSN 1529-2401
Larsson, Veronica J. et al.Mitotic spindle assembly and γ-tubulin localisation depend on the integral nuclear membrane protein Samp1Journal of Cell Science2018ISSN 1477-9137
Du Toit, André et al.The precision control of autophagic flux and vesicle dynamics—A micropattern approachCells2018ISSN 2073-4409
Bennabi, Isma et al.Shifting meiotic to mitotic spindle assembly in oocytes disrupts chromosome alignmentEMBO reports2018ISSN 1469--221X
Okumura, Masako et al.Dynein–dynactin–NuMA clusters generate cortical spindle-pulling forces as a multiarm ensembleeLife2018ISSN 2050-084X
Elting, Mary Williard et al.Mapping Load-Bearing in the Mammalian Spindle Reveals Local Kinetochore Fiber Anchorage that Provides Mechanical Isolation and RedundancyCurrent Biology2017ISSN 0960-9822
Sampson, Josephina et al.Hsp72 and Nek6 cooperate to cluster amplified centrosomes in cancer cellsCancer Research2017ISSN 1538-7445
Long, Alexandra F. et al.Hec1 Tail Phosphorylation Differentially Regulates Mammalian Kinetochore Coupling to Polymerizing and Depolymerizing MicrotubulesCurrent Biology2017ISSN 0960-9822
Kollareddy, Madhu et al.The small molecule inhibitor YK-4-279 disrupts mitotic progression of neuroblastoma cells, overcomes drug resistance and synergizes with inhibitors of mitosisCancer Letters2017ISSN 1872-7980
Hsu, Hsiang Ting et al.Measurement of lytic granule convergence after formation of an NK cell immunological synapseMethods in Molecular Biology2017ISSN 1064-3745
Magliocca, Valentina et al.Identifying the dynamics of actin and tubulin polymerization in iPSCs and in iPSC-derived neuronsOncotarget2017ISSN 1949-2553
Stojkov, Darko et al.ROS and glutathionylation balance cytoskeletal dynamics in neutrophil extracellular trap formationJournal of Cell Biology2017ISSN 1540-8140
Segal, Dagan et al.Adhesion and Fusion of Muscle Cells Are Promoted by FilopodiaDevelopmental Cell2016ISSN 1878-1551

Q1. What is STED microscopy and how does it work?

A1. STED microscopy stands for Stimulated Emission Depletion microscopy.  It is one type of super resolution microscopy which allows the capture of images with a higher resolution than conventional light microscopy which is constrained by diffraction of light.  STED uses 2 laser pulses, one is the excitation pulse which excites the fluorophore, causing it to fluoresce.  The second pulse, referred to as the STED pulse, de-excites the fluorophore via stimulated emission in an area surrounding a central focal spot that is not de-excited and thus continues to fluoresce.  This is accomplished by focusing the STED pulse into a ring shape, a so-called donut, where the center focal spot is devoid of the STED laser pulse, conferring high resolution to the fluorescent area (Fig. 1; see Ref. 1 for more details on STED microscopy).


Figure 1. STED microscopic image of microtubules labeled with SiR-tubulin in human primary dermal fibroblasts.

Q2. Why is the SiR actin (or tubulin) probe good for STED microscopy?

A2. STED microscopy offers the ability to study cellular details on a nanometermolar scale in vivo.  To take advantage of this super resolution microscopy, one must be able to select with high specificity the area to be examined using fluorescent probes.  In addition, the fluorescent probes must be bright, photostable, exhibit no or little phototoxicity, be excited and emit in the far red spectrum.  In addition, if the probe is to be used for live cell imaging (thus avoiding fixation artifacts that occur when cells are fixed), high cell permeability is necessary.  The SiR actin and tubulin probes fulfill all of these requirements.  In short, the combination of STED and SiR probes allows for unparalleled fluorescent visualization of subcellular actin and tubulin/microtubule structures and their physical characterization in living cells, (see Fig. 2 and Ref. 2). 


Figure 2. STED images of cultured rat hippocampal neurons stained with SiR-actin. Bottom image is a close-up view of part of the top image to clearly visualize actin rings (stripes) with 180 nm periodicity. Courtesy Of Elisa D'Este, MPI Biophysical Chemistry, Göttingen.

Q3. What are the filter sets for these probes?

A3. The SiR actin and tubulin probes are visualized with standard Cy5 filters.  Optimal excitation is 650 nm and emission is 670 nm.  We recommend filters with an excitation of 630 + 20 nm and an emission of 680 + 20 nm (Fig. 3).  


Figure 3. Excitation (blue) and emission (red) spectra for SiR probes.

Q4. Why do the SiR probes have a low background compared to other fluorophores?

A4. SiR probes are excited by and emit light in the near infrared/far red spectral range, thus avoiding the use of shorter wavelengths such as blue and green light that typically autofluoresce, causing higher background signals.  SiR-coupled probes possess two physical states: 1. a non-fluorescent, closed off-state (spirolactone)  and 2. an open, highly fluorescent on-state (zwitterion).  The binding of the probe to its ligand target favors the highly fluorescent open state while the free unbound probe exists in the closed, non-fluorescent state (Fig. 4).  The fluorescence amplification is 100-fold from the unbound to bound state. This results in a highly sensitive biosensor in which the majority of fluorescence occurs only in the bound state (see Refs. 3 and 4). 


Figure 4. SiR derivatives exist in equilibrium between the fluorescent zwitterionic (open) form (left structure) and the non-fluorescent spiro (closed) form (right structure).

Q5: Are the SiR probes stable at room temperature?

A5: Yes, the probes are stable at room temperature for a few days.  However, it strongly depends on the probe and the solvent.  Thus, it is recommended to store all of the probes or solutions at –20°C.


Q6: Are SiR-actin and SiR-tubulin toxic to cells?

A6: Yes, above a certain threshold both probes show some effect on cell proliferation and altered actin or microtubule dynamics.  However, the probes are orders of magnitude less toxic than their parent drug.  In HeLa cells, neither actin nor microtubule dynamics were altered at concentrations below 100 nM.  At this concentration, SiR probes efficiently label microtubules and F-actin, allowing for the capture of high signal to noise images.


Q7: Do the probes work on fixed cells?

A7: SiR-actin probes can be used with PFA-fixed cells.  SiR-actin labels F-actin in PFA-fixed cells as efficiently as phalloidin derivatives.  SiR-tubulin labels microtubules only in ethyleneglycol-bis-succinimidyl-succinate (EGS)-fixed cells.  However, a selective labeling of centrosomal microtubules of PFA-fixed cells was observed.  SiR-actin and SiR-tubulin are not suitable for methanol-fixed cells.


Q8: Is it possible to image SiR-probes by STORM?

A8: No—under the very high light intensities typically used in STORM imaging, a phototoxic effect is observed on live cells.


Q9: Which organisms and tissues are stained by SiR-probes?

A9: This list describes only cell lines, tissues, or organisms that have been reported to work.  Omission of a cell line, tissue, or organism does not mean that the SiR-probes will not work with the specific cells, tissues, or organisms.


Homo sapiens: U2OS, fibroblasts, HeLa, HUVEC, MCF-10A, HCT-116, A549, erythrocytes

Mus musculus: C2C12, IA32, skeletal muscle, primary cardiomyocyte, primary oocyte

Rattus norvegicus: primary hippocampal neurons, primary cortical neurons, NRK

Cercopithecus aethiops: COS-7

Mesocricetus auratus: BHK

Drosophila melanogaster: Notum epithelium, S2

Didelphis marsupialis: OK cells


Q10. Do SiR-probes work in 3D cell cultures?

A10: Yes, the probes are able to stain cells in a 3D growth environment.


Q11: What are the correction factors CF260 and CF280for the SiR fluorophore?

A11: CF260 = 0.116 and CF280 = 0.147



1. Hell S.W. and Wichmann J. 1994. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780-782.

2. D’Este E. et al. 2015. STED nanoscopy reveals the ubiquity of subcortical cytoskeleton periodicity in living neurons. Cell Rep. 10, 1246-1251.

3. Lukinavicius G. et al. 2013. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat. Chem. 5, 132-139.

4. Lukinavicius G. et al. 2014. Fluorogenic probes for live-cell imaging of the cytoskeleton.Nature Methods. 11, 731-733.